Police initially thought they had killed Miguel Angel Mejia because they had found documents belonging to him in the ranch where the raid took place, Oscar Naranjo, a national police chief, said on Wednesday.
The alleged drug lord's identity was later confirmed by a fingerprint check to be that of Victor Manuel Mejia, his twin brother, Naranjo said.
He also said that the police were looking for the surviving twin. "We are working intensely on his search," Naranjo said.
The brothers reportedly ran an operation called Los Mellizos (The Twins), and were considered to be Colombia's top drug traffickers.
Two members of Mejia's security unit were also killed in the operation, in which police detained three others.
On the run
Mejia and his brother Victor allegedly started off trafficking cocaine before joining Colombia's paramilitary groups.
When the paramilitaries surrendered under a government brokered deal, the two brothers went on the run.
A US court issued extradition warrants for the two in 2004, claiming at the time they had shipped almost 70 tonnes of cocaine in just two years.
Alvaro Uribe, the Colombian president, has called on police to bring down the Mejia organisation, which is thought to contain dozens of smugglers and hired killers.